That's because all the southern justices had resigned and run off to join the rebellion. I imagine that they had visions of helping establish the confederate supreme court. Boy, weren't they surprised!
Regardless, Virginia v West Virginia was a 7 to 3 decision, and by agreeing to hear it the court recognized West Virginia's status as a state.
Actually, it looks like 3 Southern justices remained on the U.S. Supreme Court until their deaths (including Roger Taney, who died in 1864), one died in 1860 but was replaced by a Lincoln nominee rather than by a Buchanan nominee, and one resigned to go home to his state. There was also one justice from Ohio who died during this period.